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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DFP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DFP_1.66.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DFP.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DFP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DFP’ version ‘1.66.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DFP’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotDiscriminantFuzzyPattern: warning in matrix(x, nr = ly, nc = lx,
  byrow = TRUE): partial argument match of 'nr' to 'nrow'
plotDiscriminantFuzzyPattern: warning in matrix(x, nr = ly, nc = lx,
  byrow = TRUE): partial argument match of 'nc' to 'ncol'
plotDiscriminantFuzzyPattern: warning in matrix(y, nr = ly, nc = lx):
  partial argument match of 'nr' to 'nrow'
plotDiscriminantFuzzyPattern: warning in matrix(y, nr = ly, nc = lx):
  partial argument match of 'nc' to 'ncol'
.plotGeneMF: no visible global function definition for ‘curve’
.plotGeneMF: no visible binding for global variable ‘x’
.plotGeneMF: no visible global function definition for ‘abline’
.plotGeneMF: no visible global function definition for ‘palette’
.plotGeneMF: no visible global function definition for ‘rainbow’
.plotGeneMF: no visible global function definition for ‘legend’
calculateFuzzyPatterns: no visible global function definition for
  ‘head’
discretizeExpressionValues: no visible global function definition for
  ‘head’
discriminantFuzzyPattern: no visible global function definition for
  ‘head’
plotDiscriminantFuzzyPattern: no visible global function definition for
  ‘image’
plotDiscriminantFuzzyPattern: no visible global function definition for
  ‘par’
plotDiscriminantFuzzyPattern: no visible global function definition for
  ‘axis’
plotDiscriminantFuzzyPattern: no visible global function definition for
  ‘text’
plotMembershipFunctions: no visible global function definition for
  ‘par’
readCSV: no visible global function definition for ‘read.table’
readCSV: no visible global function definition for ‘head’
Undefined global functions or variables:
  abline axis curve head image legend palette par rainbow read.table
  text x
Consider adding
  importFrom("grDevices", "palette", "rainbow")
  importFrom("graphics", "abline", "axis", "curve", "image", "legend",
             "par", "text")
  importFrom("utils", "head", "read.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'DFP-package.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’

Non-topic package-anchored link(s) in Rd file 'calculateDiscriminantFuzzyPattern.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’

Non-topic package-anchored link(s) in Rd file 'calculateFuzzyPatterns.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’

Non-topic package-anchored link(s) in Rd file 'calculateMembershipFunctions.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’

Non-topic package-anchored link(s) in Rd file 'discretizeExpressionValues.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’

Non-topic package-anchored link(s) in Rd file 'discriminantFuzzyPattern.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’

Non-topic package-anchored link(s) in Rd file 'plotMembershipFunctions.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’

Non-topic package-anchored link(s) in Rd file 'readCSV.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’

Non-topic package-anchored link(s) in Rd file 'rmadataset.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’

Non-topic package-anchored link(s) in Rd file 'showDiscreteValues.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'showFuzzyPatterns.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/DFP.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DFP
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘DFP’ ...
** this is package ‘DFP’ version ‘1.66.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DFP)